Discordance of the PAM50 Intrinsic Subtypes Compared with Immunohistochemistry-Based Surrogate in Breast Cancer Patients: Potential Implication of Genomic Alterations of Discordance

Abstract

Purpose: We aimed to analyze the discordance between immunohistochemistry (IHC)-based surrogate subtyping and PAM50 intrinsic subtypes and to assess overall survival (OS) according to discordance.

Materials and methods: A total of 607 patients were analyzed. Hormone receptor (HR) expression was evaluated by IHC, and human epidermal growth factor receptor 2 (HER2) expression was analyzed by IHC and/or fluorescence in situ hybridization. PAM50 intrinsic subtypes were determined according to 50 cancer genes using the NanoString nCounter Analysis System. We matched concordant tumor as luminal A and HR+/HER2-, luminal B and HR+/HER2+, HR-/HER2+ and HER2-enriched, and triple-negative breast cancer (TNBC) and normal- or basal-like. We used Ion Ampliseq Cancer Panel v2 was used to identify the genomic alteration related with discordance. The Kaplan-Meier method was used to estimate OS.

Results: In total, 233 patients (38.4%) were discordant between IHC-based subtype and PAM50 intrinsic subtype. Using targeted sequencing, we detected somatic mutation-related discordant breast cancer including the VHL gene in the HR+/HER2- group (31% in concordant group, 0% in discordant group, p=0.03) and the IDH and RET genes (7% vs. 12%, p=0.02 and 0% vs. 25%, p=0.02, respectively) in the TNBC group. Among the luminal A/B patients with a discordant result had significantly worse OS (median OS, 73.6 months vs. not reached; p < 0.001), and among the patients with HR positivity, the basal-like group as determined by PAM50 showed significantly inferior OS compared to other intrinsic subtypes (5-year OS rate, 92.2% vs. 75.6%; p=0.01).

Conclusion: A substantial portion of patients showed discrepancy between IHC subtype and PAM50 intrinsic subtype in our study. The survival analysis demonstrated that current IHC-based classification could mislead the treatment and result in poor outcome. Current guidelines for IHC might be updated accordingly.

Keywords: Breast neoplasms; Immunohistochemistry; PAM50.

Fig. 1.

Distribution of the PAM50 intrinsic subtypes within each immunohistochemistry-based group. HR, hormone receptor; HER2, human epidermal growth factor receptor 2; TNBC, triple-negative breast cancer.

Fig. 2.

Mutation pattern according to the frequency of 50 cancer-related genes: mutation map of concordant group (A) and mutation map of discordant group (B). HR, hormone receptor; HER2, human epidermal growth factor receptor 2; TNBC, triple-negative breast cancer.

Fig. 3.

The prevalence of mutated genes in concordant/discordant tumors of hormone receptor (HR)+/human epidermal growth factor receptor 2 (HER2)– (A), HR+/HER2+ (B), HR–/HER2+ (C), and TNBC (D). ^*p < 0.05.

Fig. 4.

Re-classification for hierarchical clustering of data based on the incidence of mutated genes in concordant and discordant tumors. (A) The dendrogram of discordant pattern based on mutated genes using 10,000 multi-scale bootstrap re-sampling; blue letter: approximately unbiased (AU) values, red letters: bootstrap probability (BP) values. Clusters with AU values greater than 0.95 are highlighted with a red rectangle and are strongly supported. (B) The heatmap of discordant pattern with mutation incidence.

Fig. 5.

Kaplan-Meier curve of overall survival (OS) according to discordance. (A) All patients (n=607). (B) OS in basal-like and non-basal-like types in hormone receptor (HR)+ patients (n=343). (C) OS in HR+ and HR– by immunohistochemistry in luminal A or B patients (n=283). CI, confidence interval.